Download MendeleyA novel DNA recognition mode by the NF-kappa B p65 homodimer.
Chen, Y.Q., Ghosh, S., Ghosh, G.(1998) Nat Struct Biol 5: 67-73
- PubMed: 9437432
- DOI: https://doi.org/10.1038/nsb0198-67
- Primary Citation of Related Structures:
1RAM, 2RAM - PubMed Abstract:
The crystal structure of the NF-kappa B p65 (RelA) homodimer in complex with a DNA target has been determined to 2.4 A resolution. The two p65 subunits are not symmetrically disposed on the DNA target. The homodimer should optimally bind to a pseudo-palindromic nine base pair target with each subunit recognizing a 5'GGAA-3' half site separated by a central A-T base pair. However, one of the subunits (subunit B) encounters a half site of 5'-GAAA-3'. The single base-pair change from G-C to A-T results in highly unfavorable interactions between this half site and the base contacting protein residues in subunit B, which leads to an 18 degrees rotation of the N-terminal terminal domain from its normal conformation. Remarkably, subunit B retains all the interactions with the sugar phosphate backbone of the DNA target. This mode of interaction allows the NF-kappa B p65 homodimer to recognize DNA targets containing only one cognate half site. Differences in the sequence of the other half site provide variations in conformation and affinity of the complex.
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0359, USA.
Organizational Affiliation:
